Automatic and manual functional annotation in a distributed web service environment

While the number of genomic sequences becoming available is increasing exponentially, most genes are not functionally well characterized. Finding out more about the function of a gene and about functional relationships between genes will be the next big bottleneck in the post-genomic era. On the one hand improved pipelines and tools are needed in this context, because running experiments for all predicted genes is not feasible. On the other hand manual curation of the automatic predictions is necessary to judge the reliability of the automatic annotation and to get a more comprehensive view on the function of each individual gene. For the automatic functional annotation often a homology based function transfer from functionally characterized genes is applied using methods like Blast. However, this approach has many drawbacks and makes systematic errors by not taking care of speciation and duplication events. Phylogenomics has shown to improve the functional prediction accuracy by taking the evolutionary history of genes in a phylogenetic tree context into account. In this thesis the manual process from the assembly of the DNA sequence to the functional characterization of genes and the identification and comparison of shared syntenic regions, including the identification of candidate genes for pathogen resistance in potato chromosome V, is explained and problems discussed. To improve the automatic functional annotation in genome projects, a phylogenomic pipeline, which includes SIFTER one of the best phylogenomic tools in this area, is introduced, improved and tested in the Medicago truncatula, Sorghum bicolor and Solanum lycopersicum genome projects. To obtain new candidate genes for the development of new drugs and crop protection products, non-plant specific genes, like the transferrin family which is not known in plants yet, are extracted from the M. truncatula and S. bicolor genomes and further investigated. For further improvement of the annotation, a new phylogenomic approach is developed. This approach makes use of annotated functional attributes to calculate the functional mutation rate between genes and groups of genes in a phylogenetic tree and to find out if the function of a gene can be transferred or not. The new approach is integrated into the SIFTER tool and tested on the blue-light photoreceptor/photolyase family and on a test set of manually curated Arabidopsis thaliana genes. Using both test sets the prediction accuracy could be significantly improved and a more comprehensive view on the gene function could be obtained. But because still no tool is able to annotate all functions of a gene with 100% accuracy, I introduce a system for manual functional annotation, called AFAWE. AFAWE runs different web services for the functional annotation and displays the results and intermediate results in a comprehensive web interface that facilitates comparison. It can be used for any organism and any kind of gene. The inputs are the amino acid sequence and the corresponding organism. Because of its flexible structure, new web services and workflows can be easily integrated. Besides Blast searches against different databases and protein domain prediction tools, AFAWE also includes the phylogenomic pipeline. Different filters help to identify trustworthy results from each analysis. Furthermore a detailed manual annotation can be assigned to each protein, which will be used to update the functional annotation in public databases like MIPSPlantsDB

Numerical Investigation of the Aerodynamic Vibration Excitation of High-Pressure Turbine Rotors

The design parameters axial gap and stator count of highpressure turbine stages are evaluated numerically towards theirinfluence on the unsteady aerodynamic excitation of rotorblades. Of particular interest is if and how unsteadyaerodynamic considerations in the design could reduce the riskofhigh cycle fatigue (HCF) failures of the turbine rotor. A well-documented 2D/Q3D non-linear unsteady code (UNSFLO)is chosen to perform the stage flow analyses. The evaluatedresults are interpreted as aerodynamic excitation mechanisms onstream sheets neglecting 3D effects. Mesh studies andvalidations against measurements and 3D computations provideconfidence in the unsteady results. Three test cases areanalysed. First, a typical aero-engine high pressure turbinestage is studied at subsonic and transonic flow conditions,with four axial gaps (37% - 52% of cax,rotor) and two statorconfigurations (43 and 70 NGV). Operating conditions areaccording to the resonant conditions of the blades used inaccompanied experiments. Second, a subsonic high pressureturbine intended to drive the turbopump of a rocket engine isinvestigated. Four axial gap variations (10% - 29% ofcax,rotor) and three stator geometry variations are analysed toextend and generalise the findings made on the first study.Third, a transonic low pressure turbine rotor, known as theInternational Standard Configuration 11, has been modelled tocompute the unsteady flow due to blade vibration and comparedto available experimental data. Excitation mechanisms due to shock, potential waves andwakes are described and related to the work found in the openliterature. The strength of shock excitation leads to increasedpressure excitation levels by a factor 2 to 3 compared tosubsonic cases. Potential excitations are of a typical wavetype in all cases, differences in the propagation direction ofthe waves and the wave reflection pattern in the rotor passagelead to modifications in the time and space resolved unsteadypressures on the blade surface. The significant influence ofoperating conditions, axial gap and stator size on the wavepropagation is discussed on chosen cases. The wake influence onthe rotorblade unsteady pressure is small in the presentevaluations, which is explicitly demonstrated on the turbopumpturbine by a parametric study of wake and potentialexcitations. A reduction in stator size (towards R≈1)reduces the potential excitation part so that wake andpotential excitation approach in their magnitude. Potentials to reduce the risk of HCF excitation in transonicflow are the decrease of stator exit Mach number and themodification of temporal relations between shock and potentialexcitation events. A similar temporal tuning of wake excitationto shock excitation appears not efficient because of the smallwake excitation contribution. The increase of axial gap doesnot necessarily decrease the shock excitation strength neitherdoes the decrease of vane size because the shock excitation mayremain strong even behind a smaller stator. The evaluation ofthe aerodynamic excitation towards a HCF risk reduction shouldonly be done with regard to the excited mode shape, asdemonstrated with parametric studies of the mode shapeinfluence on excitability. Keywords:Aeroelasticity, Aerodynamics, Stator-RotorInteraction, Excitation Mechanism, Unsteady Flow Computation,Forced Response, High Cycle Fatigue, Turbomachinery,Gas-Turbine, High-Pressure Turbine, Turbopump, CFD, DesignNR 2014080

Steam temperature stability in a direct steam generation solar power Plant

Direct steam generation (DSG) is one alternative to the current oil-based parabolic trough solar thermal power plants. Within the German research project ITES, the dynamic behavior of a DSG collector field and the interactions with the conventional power block are assessed in detail. A transient solar field model developed by DLR is used to simulate the steam temperature behavior. Artificial irradiance disturbances as well as real irradiance data are used as input to the system. The resulting main steam temperature gradients are then analyzed by Siemens considering the standards for steam turbines. This paper presents the transient simulation results of the steam temperature as well as the corresponding results of the steam turbine analysis. It is found that the occurring temperature gradients are challenging for a safe turbine operation, if a conservative control system is used. Therefore, the use of an additional thermal inertia to stabilize the steam temperature is suggested. Its impact is also analyzed and discussed in this paper

Transesterification of rapeseed oil catalyzed by sodium doped calcium oxide

The aim of this study was to find and use a heterogeneous catalyst to catalyze the transesterification reaction of biodiesel. The purpose of this is to have a more sustainable production of biodiesel which uses fewer chemicals and can reuse the catalyst easily. Our team chose a base catalyst of calcium oxide (CaO) based on early research but with a change of doping the base catalyst with sodium, thus making sodium doped calcium oxide (Na-CaO). The catalyst was synthesized using calcium hydroxide and sodium hydroxide as precursors. The sodium concentration was chosen to be at 3 weight%. The main part of the study was on testing the efficiency of the catalyst and determining at which conditions the reaction performs best. The best conditions for the catalyst were found at 60 °C and the ratio of rapeseed oil to methanol was 1:9. The mass concentration of the catalyst was 2 weight% and the reaction time was 2 hours. These conditions resulted in a biodiesel yield of 97,6 %.Studien som gjordes gick ut på att tillverka en heterogen katalysator för att katalysera transesterifiering reaktionen för biodieseltillverkning. Syftet med detta är att ha en mer hållbar produktion som använder sig utav färre kemikalier och samtidigt kan återanvända katalysatorn. Valet av katalysator skedde efter värdering av äldre studier och basen för katalysatorn valdes till kalciumoxid (CaO), med en ändring av att dopa denna med natrium, det vill säga natriumdopad kalciumoxid (Na-CaO). Katalysatorn syntetiserades utav kalciumhydroxid och natriumhydroxid. Koncentrationen av natriumet låg vid 3 vikt%. Nästa del utav studien gick ut på att testa den syntetiserade katalysatorn och hitta de bästa betingelserna för bästa utbyte av biodiesel. De bästa betingelserna var vid temperaturen 60 °C och ett förhållande mellan rapsolja och metanol på 1:9, där masshalten av katalysator var 2 vikts% gentemot oljan och reaktionstiden var 2 timmar. Detta gav ett utbyte på 97,6 %

Parametric studies of the aerodynamic excitation in high pressure turbines

Numerical and experimental studies are performed on the influence of several key parameters on the aerodynamic exitation of a high-pressure turbine rotor blade row due to the upstream stator row. In order to change the vane passing frequency two stators with similar vane shapes and identical exit Mach number and exit flow angle are used. To be able to separate subsonic and transonic stator induced flow distortions data is recorded at two different flow regimes. The axial gap between stator and rotor is varied as well. Experiments were run in a closed loop high speed annular wind tunnel. Unsteady velocity data were measured with a three-dimensional Laser-Two-Focus anemometer between stator and rotor and downstream of the rotor. The unsteady part of the instantaneous velocity, the gust, is split into streamwise, transverse and radial components and harmonically decomposed. This data is compared to numerical results obtained with a quasi 3D method (UNSFLO) and analysed regarding two aspects: the dependency of the gust on the changed parameters and the impact of the gust on the forcing function (blade excitation pressures)

NUMERICAL UNSTEADY FLOW ANALYSIS OF A TURBINE STAGE WITH EXTREMELY LARGE BLADE LOADS

ABSTRACT This paper presents the detailed numerical analysis including parametric studies on the aerodynamic excitation mechanisms in a turbine stage due to the unsteady stator-rotor interaction. The work is part of the pre-design study of a high pressure subsonic turbine for a rocket engine turbopump. The pressure level in such turbines can be remarkably high (in this case 54 MPa inlet total pressure). Hence, large unsteady rotor blade loads can be expected, which impose difficult design requirements. The parameter studies are performed at midspan with the numerical flow solver UNSFLO, a 2D/Q3D unsteady hybrid Euler/Navier-Stokes solver. Comparisons to 2D and steady 3D results obtained with a fully viscous solver, VOLSOL, are made. The investigated design parameters are the axial gap (~8%-29% of rotor axial chord length) and the stator vane size and count (stator-rotor pitch ratio ~1-2.75). For the nominal case the numerical solution is analyzed regarding the contributions of potential and vortical flow disturbances at the rotor inlet using rotor gust computations. It was found that gust calculations were not capable to capture the complexity of the detected excitation mechanisms, but the possibility to reduce excitations by enforcing cancellation of the vortical and potential effects has been elaborated. The potential excitation mechanism in the present turbine stage is found dominant compared to relatively small and local wake excitation effects. The parameter studies indicate design recommendations for the axial gap and the stator size regarding the unsteady rotor load

Comparison of Models to Predict Low Engine Order Excitation in a High Pressure Turbine Stage

The paper compares three numerical strategies to predict the aerodynamic rotor excitation sources of "Low Engine Order" (LEO) in a high-pressure turbine stage. Main focus is laid on methods to compute the stator exit flow. The aim is to evaluate computationally cheap approaches to avoid modelling the whole circumference of the stator. A single passage viscous strategy, a single passage inviscid linear blade movement strategy and a viscous multi passage sector strategy are compared and evaluated. The assessment of the prediction quality is made by comparison of the computed stator exit flow to experimental data. The main result is that only the global behaviour of the stator exit flow is estimated right, both level and amplitude of Mach number and pressure are computed with poor agreement to experiments. Future evaluations of the resulting rotor excitation pressure are needed to estimate the level of necessary agreement to give acceptable predictions of the low engine order forced response